Various changes required for the new harmony pipeline. The most important changes are listed below:

• Add testing, including various tests to make sure the program aborts on unsupported input
• Change the way the vcf files are compared to allow comparisons between different REF/ALT values
• Add support for comparing partial calls, e.g. A/A vs A/. is counted as 1 concordant allele, and 1 'no call'
• Add support for filtering on RGQ instead of GQ when a site is called as homref
• Write discordant variants from the 'call' VCF file to a valid VCF file